4QI2
X-ray structure of the ROQ domain from murine Roquin-1 in complex with a 23-mer Tnf-CDE RNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4QI0 | pdb entry 4QI0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 200 mM NaCl, 100 mM Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.56 | α = 105.68 |
b = 60.41 | β = 101.36 |
c = 84.37 | γ = 95.72 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2014-01-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 1.03321 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 3 | 50 | 95.7 | 0.07 | 13.9 | 19951 | 19951 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3 | 3.08 | 96.9 | 0.513 | 3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 4QI0 | 3 | 50 | 18931 | 18931 | 1020 | 95.82 | 0.20549 | 0.20316 | 0.24679 | RANDOM | 77.711 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
6.29 | 6.88 | -1.27 | -5.25 | 0.73 | -1.69 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.798 |
r_dihedral_angle_3_deg | 18.243 |
r_dihedral_angle_4_deg | 13.619 |
r_long_range_B_other | 13.417 |
r_long_range_B_refined | 13.416 |
r_scangle_other | 9.992 |
r_mcangle_it | 8.88 |
r_mcangle_other | 8.879 |
r_scbond_it | 6.637 |
r_scbond_other | 6.633 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4895 |
Nucleic Acid Atoms | 1576 |
Solvent Atoms | 32 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |